Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =14;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 25 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('time in component environment (millisecond)');
LEGEND_STATES(:,1) = strpad('V in component membrane (millivolt)');
LEGEND_CONSTANTS(:,1) = strpad('C in component membrane (picoF)');
LEGEND_CONSTANTS(:,2) = strpad('i_app in component membrane (picoA)');
LEGEND_ALGEBRAIC(:,12) = strpad('i_NaP in component persistent_sodium_current (picoA)');
LEGEND_ALGEBRAIC(:,5) = strpad('i_Na in component fast_sodium_current (picoA)');
LEGEND_ALGEBRAIC(:,9) = strpad('i_K in component potassium_current (picoA)');
LEGEND_ALGEBRAIC(:,10) = strpad('i_KS in component slow_potassium_current (picoA)');
LEGEND_ALGEBRAIC(:,13) = strpad('i_L in component leakage_current (picoA)');
LEGEND_ALGEBRAIC(:,14) = strpad('i_tonic_e in component tonic_current (picoA)');
LEGEND_CONSTANTS(:,3) = strpad('E_Na in component fast_sodium_current (millivolt)');
LEGEND_CONSTANTS(:,4) = strpad('g_Na in component fast_sodium_current (nanoS)');
LEGEND_ALGEBRAIC(:,1) = strpad('m_infinity in component fast_sodium_current_m_gate (dimensionless)');
LEGEND_STATES(:,2) = strpad('n in component fast_sodium_current_n_gate (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('theta_m in component fast_sodium_current_m_gate (millivolt)');
LEGEND_CONSTANTS(:,6) = strpad('sigma_m in component fast_sodium_current_m_gate (millivolt)');
LEGEND_ALGEBRAIC(:,2) = strpad('n_infinity in component fast_sodium_current_n_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('tau_n in component fast_sodium_current_n_gate (millisecond)');
LEGEND_CONSTANTS(:,7) = strpad('tau_n_max in component fast_sodium_current_n_gate (millisecond)');
LEGEND_CONSTANTS(:,8) = strpad('theta_n in component fast_sodium_current_n_gate (millivolt)');
LEGEND_CONSTANTS(:,9) = strpad('sigma_n in component fast_sodium_current_n_gate (millivolt)');
LEGEND_CONSTANTS(:,10) = strpad('E_K in component potassium_current (millivolt)');
LEGEND_CONSTANTS(:,11) = strpad('g_K in component potassium_current (nanoS)');
LEGEND_STATES(:,3) = strpad('n in component potassium_current_n_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('n_infinity in component potassium_current_n_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('tau_n in component potassium_current_n_gate (millisecond)');
LEGEND_CONSTANTS(:,12) = strpad('tau_n_max in component potassium_current_n_gate (millisecond)');
LEGEND_CONSTANTS(:,13) = strpad('theta_n in component potassium_current_n_gate (millivolt)');
LEGEND_CONSTANTS(:,14) = strpad('sigma_n in component potassium_current_n_gate (millivolt)');
LEGEND_CONSTANTS(:,15) = strpad('g_KS in component slow_potassium_current (nanoS)');
LEGEND_STATES(:,4) = strpad('k in component slow_potassium_current_k_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('k_infinity in component slow_potassium_current_k_gate (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('tau_k in component slow_potassium_current_k_gate (millisecond)');
LEGEND_CONSTANTS(:,16) = strpad('tau_k_max in component slow_potassium_current_k_gate (millisecond)');
LEGEND_CONSTANTS(:,17) = strpad('theta_k in component slow_potassium_current_k_gate (millivolt)');
LEGEND_CONSTANTS(:,18) = strpad('sigma_k in component slow_potassium_current_k_gate (millivolt)');
LEGEND_CONSTANTS(:,19) = strpad('g_NaP in component persistent_sodium_current (nanoS)');
LEGEND_ALGEBRAIC(:,11) = strpad('m_infinity in component persistent_sodium_current_m_gate (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('theta_m in component persistent_sodium_current_m_gate (millivolt)');
LEGEND_CONSTANTS(:,21) = strpad('sigma_m in component persistent_sodium_current_m_gate (millivolt)');
LEGEND_CONSTANTS(:,22) = strpad('g_L in component leakage_current (nanoS)');
LEGEND_CONSTANTS(:,23) = strpad('E_L in component leakage_current (millivolt)');
LEGEND_CONSTANTS(:,24) = strpad('g_tonic_e in component tonic_current (nanoS)');
LEGEND_CONSTANTS(:,25) = strpad('E_syn_e in component tonic_current (millivolt)');
LEGEND_RATES(:,1) = strpad('d/dt V in component membrane (millivolt)');
LEGEND_RATES(:,2) = strpad('d/dt n in component fast_sodium_current_n_gate (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt n in component potassium_current_n_gate (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt k in component slow_potassium_current_k_gate (dimensionless)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
STATES(:,1) = -55.0;
CONSTANTS(:,1) = 21.0;
CONSTANTS(:,2) = 0.0;
CONSTANTS(:,3) = 50.0;
CONSTANTS(:,4) = 28.0;
STATES(:,2) = 0.01;
CONSTANTS(:,5) = -34.0;
CONSTANTS(:,6) = -5.0;
CONSTANTS(:,7) = 10.0;
CONSTANTS(:,8) = -29.0;
CONSTANTS(:,9) = -4.0;
CONSTANTS(:,10) = -85.0;
CONSTANTS(:,11) = 11.2;
STATES(:,3) = 0.01;
CONSTANTS(:,12) = 10.0;
CONSTANTS(:,13) = -29.0;
CONSTANTS(:,14) = -4.0;
CONSTANTS(:,15) = 5.6;
STATES(:,4) = 0.22;
CONSTANTS(:,16) = 10000.0;
CONSTANTS(:,17) = -38.0;
CONSTANTS(:,18) = -6.0;
CONSTANTS(:,19) = 2.8;
CONSTANTS(:,20) = -40.0;
CONSTANTS(:,21) = -6.0;
CONSTANTS(:,22) = 2.8;
CONSTANTS(:,23) = -50.0;
CONSTANTS(:,24) = 0.0;
CONSTANTS(:,25) = 0.0;
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,2) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,8))./CONSTANTS(:,9)));
ALGEBRAIC(:,6) = CONSTANTS(:,7)./cosh((STATES(:,1) - CONSTANTS(:,8))./( 2.00000.*CONSTANTS(:,9)));
RATES(:,2) = (ALGEBRAIC(:,2) - STATES(:,2))./ALGEBRAIC(:,6);
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,13))./CONSTANTS(:,14)));
ALGEBRAIC(:,7) = CONSTANTS(:,12)./cosh((STATES(:,1) - CONSTANTS(:,13))./( 2.00000.*CONSTANTS(:,14)));
RATES(:,3) = (ALGEBRAIC(:,3) - STATES(:,3))./ALGEBRAIC(:,7);
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,17))./CONSTANTS(:,18)));
ALGEBRAIC(:,8) = CONSTANTS(:,16)./cosh((STATES(:,1) - CONSTANTS(:,17))./( 2.00000.*CONSTANTS(:,18)));
RATES(:,4) = (ALGEBRAIC(:,4) - STATES(:,4))./ALGEBRAIC(:,8);
ALGEBRAIC(:,11) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,20))./CONSTANTS(:,21)));
ALGEBRAIC(:,12) = CONSTANTS(:,19).*ALGEBRAIC(:,11).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,1) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,5))./CONSTANTS(:,6)));
ALGEBRAIC(:,5) = CONSTANTS(:,4).*power(ALGEBRAIC(:,1), 3.00000).*(1.00000 - STATES(:,2)).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = CONSTANTS(:,11).*power(STATES(:,3), 4.00000).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,10) = CONSTANTS(:,15).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,13) = CONSTANTS(:,22).*(STATES(:,1) - CONSTANTS(:,23));
ALGEBRAIC(:,14) = CONSTANTS(:,24).*(STATES(:,1) - CONSTANTS(:,25));
RATES(:,1) = ( - (ALGEBRAIC(:,12)+ALGEBRAIC(:,10)+ALGEBRAIC(:,5)+ALGEBRAIC(:,9)+ALGEBRAIC(:,13)+ALGEBRAIC(:,14))+CONSTANTS(:,2))./CONSTANTS(:,1);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,2) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,8))./CONSTANTS(:,9)));
ALGEBRAIC(:,6) = CONSTANTS(:,7)./cosh((STATES(:,1) - CONSTANTS(:,8))./( 2.00000.*CONSTANTS(:,9)));
ALGEBRAIC(:,3) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,13))./CONSTANTS(:,14)));
ALGEBRAIC(:,7) = CONSTANTS(:,12)./cosh((STATES(:,1) - CONSTANTS(:,13))./( 2.00000.*CONSTANTS(:,14)));
ALGEBRAIC(:,4) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,17))./CONSTANTS(:,18)));
ALGEBRAIC(:,8) = CONSTANTS(:,16)./cosh((STATES(:,1) - CONSTANTS(:,17))./( 2.00000.*CONSTANTS(:,18)));
ALGEBRAIC(:,11) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,20))./CONSTANTS(:,21)));
ALGEBRAIC(:,12) = CONSTANTS(:,19).*ALGEBRAIC(:,11).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,1) = 1.00000./(1.00000+exp((STATES(:,1) - CONSTANTS(:,5))./CONSTANTS(:,6)));
ALGEBRAIC(:,5) = CONSTANTS(:,4).*power(ALGEBRAIC(:,1), 3.00000).*(1.00000 - STATES(:,2)).*(STATES(:,1) - CONSTANTS(:,3));
ALGEBRAIC(:,9) = CONSTANTS(:,11).*power(STATES(:,3), 4.00000).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,10) = CONSTANTS(:,15).*STATES(:,4).*(STATES(:,1) - CONSTANTS(:,10));
ALGEBRAIC(:,13) = CONSTANTS(:,22).*(STATES(:,1) - CONSTANTS(:,23));
ALGEBRAIC(:,14) = CONSTANTS(:,24).*(STATES(:,1) - CONSTANTS(:,25));
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end